derfinder: Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
Version 1.10.4

This package provides functions for annotation-agnostic differential expression analysis of RNA-seq data. Two implementations of the DER Finder approach are included in this package: (1) single base-level F-statistics and (2) DER identification at the expressed regions-level. The DER Finder approach can also be used to identify differentially bounded ChIP-seq peaks.

Browse man pages Browse package API and functions Browse package files

AuthorLeonardo Collado-Torres [aut, cre], Alyssa C. Frazee [ctb], Andrew E. Jaffe [aut], Jeffrey T. Leek [aut, ths]
Bioconductor views ChIPSeq DifferentialExpression DifferentialPeakCalling RNASeq Sequencing Software
Date of publicationNone
MaintainerLeonardo Collado-Torres <lcollado@jhu.edu>
LicenseArtistic-2.0
Version1.10.4
URL https://github.com/lcolladotor/derfinder
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("derfinder")

Man pages

analyzeChr: Run the derfinder analysis on a chromosome
annotateRegions: Assign genomic states to regions
calculatePvalues: Calculate p-values and identify regions
calculateStats: Calculate F-statistics at base pair resolution from a loaded...
coerceGR: Coerce the coverage to a GRanges object for a given sample
collapseFullCoverage: Collapse full coverage information for efficient quantile...
coverageToExon: Extract coverage information for exons
createBw: Export coverage to BigWig files
createBwSample: Create a BigWig file with the coverage information for a...
define_cluster: Define a cluster to use.
derfinder-deprecated: Deprecated functions in package 'derfinder'
derfinder-package: Annotation-agnostic differential expression analysis of...
extendedMapSeqlevels: Change naming style for a set of sequence names
filterData: Filter the positions of interest
findRegions: Find non-zero regions in a Rle
fullCoverage: Load the unfiltered coverage information from a group of BAM...
genomeData: Genome samples processed data
genomeDataRaw: Genome samples processed data
genomeFstats: F-statistics for the example data
genomeInfo: Genome samples information
genomeRegions: Candidate DERs for example data
genomicState: Genomic State for Hsapiens.UCSC.hg19.knownGene
getRegionCoverage: Extract coverage information for a set of regions
getTotalMapped: Calculate the total number of mapped reads
loadCoverage: Load the coverage information from a group of BAM files
makeGenomicState: Obtain the genomic state per region from annotation
makeModels: Build model matrices for differential expression
mergeResults: Merge results from different chromosomes
preprocessCoverage: Transform and split the data
railMatrix: Identify regions data by a coverage filter and get a count...
rawFiles: Construct full paths to a group of raw input files
regionMatrix: Identify regions data by a coverage filter and get a count...
sampleDepth: Calculate adjustments for library size

Functions

REDUCER Source code
advancedArg Man page Source code
advanced_argument Source code
analyzeChr Man page Source code
annotateRegions Man page Source code
bamMAPPER Source code
calcFstatCutoff Source code
calcPval Source code
calcQuantile Source code
calculateFWER Source code
calculatePvalues Man page Source code
calculateStats Man page Source code
clusterMakerRle Source code
coerceGR Man page Source code
collapseFullCoverage Man page Source code
coverageToExon Man page Source code
coverageToExonStrandStep Source code
createBw Man page Source code
createBwSample Man page Source code
define_cluster Man page Source code
derfinder-deprecated Man page
derfinder-package Man page
extendedMapSeqlevels Man page Source code
filterData Man page Source code
findRegions Man page Source code
fullCoverage Man page Source code
genomeData Man page
genomeDataRaw Man page
genomeFstats Man page
genomeInfo Man page
genomeRegions Man page
genomicState Man page
getRegionCoverage Man page Source code
getSegmentsRle Source code
getTotalMapped Man page Source code
loadCoverage Man page Source code
loadCoverageBAM Source code
loadCoverageBigWig Source code
load_fullCov Source code
makeGenomicState Man page Source code
makeModels Man page Source code
mergeResults Man page Source code
preprocessCoverage Man page Source code
railMatChrRegion Source code
railMatChrRegionCov Source code
railMatrix Man page Source code
railMatrixChr Source code
rawFiles Man page Source code
regionMatrix Man page Source code
regionMatrixByChr Source code
runFunFormal Source code
sampleCorradaAdj Source code
sampleDepth Man page Source code
selectBestGuess Source code
smoothFstatsFun Source code
smootherFstats Source code
writeRegs Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/Deprecated.R
R/analyzeChr.R
R/annotateRegions.R
R/calculatePvalues.R
R/calculateStats.R
R/coerceGR.R
R/collapseFullCoverage.R
R/coverageToExon.R
R/createBw.R
R/createBwSample.R
R/define_cluster.R
R/derfinder-package.R
R/extendedMapSeqlevels.R
R/filterData.R
R/findRegions.R
R/fullCoverage.R
R/genomeData-data.R
R/genomeDataRaw-data.R
R/genomeFstats-data.R
R/genomeInfo-data.R
R/genomeRegions-data.R
R/genomicState-data.R
R/getRegionCoverage.R
R/getTotalMapped.R
R/loadCoverage.R
R/makeGenomicState.R
R/makeModels.R
R/mergeResults.R
R/preprocessCoverage.R
R/railMatrix.R
R/rawFiles.R
R/regionMatrix.R
R/sampleDepth.R
R/utils.R
README.md
build
build/vignette.rds
data
data/genomeData.RData
data/genomeDataRaw.RData
data/genomeFstats.RData
data/genomeInfo.RData
data/genomeRegions.RData
data/genomicState.RData
inst
inst/CITATION
inst/doc
inst/doc/derfinder-quickstart.R
inst/doc/derfinder-quickstart.Rmd
inst/doc/derfinder-quickstart.html
inst/doc/derfinder-users-guide.R
inst/doc/derfinder-users-guide.Rmd
inst/doc/derfinder-users-guide.html
inst/extdata
inst/extdata/chr21
inst/extdata/chr21/annotation.Rdata
inst/extdata/chr21/coveragePrep.Rdata
inst/extdata/chr21/fstats.Rdata
inst/extdata/chr21/optionsStats.Rdata
inst/extdata/chr21/regions.Rdata
inst/extdata/chr21/timeinfo.Rdata
inst/extdata/genomeData
inst/extdata/genomeData/ERR009101_accepted_hits.bam
inst/extdata/genomeData/ERR009101_accepted_hits.bam.bai
inst/extdata/genomeData/ERR009102_accepted_hits.bam
inst/extdata/genomeData/ERR009102_accepted_hits.bam.bai
inst/extdata/genomeData/ERR009105_accepted_hits.bam
inst/extdata/genomeData/ERR009105_accepted_hits.bam.bai
inst/extdata/genomeData/ERR009107_accepted_hits.bam
inst/extdata/genomeData/ERR009107_accepted_hits.bam.bai
inst/extdata/genomeData/ERR009108_accepted_hits.bam
inst/extdata/genomeData/ERR009108_accepted_hits.bam.bai
inst/extdata/genomeData/ERR009112_accepted_hits.bam
inst/extdata/genomeData/ERR009112_accepted_hits.bam.bai
inst/extdata/genomeData/ERR009115_accepted_hits.bam
inst/extdata/genomeData/ERR009115_accepted_hits.bam.bai
inst/extdata/genomeData/ERR009116_accepted_hits.bam
inst/extdata/genomeData/ERR009116_accepted_hits.bam.bai
inst/extdata/genomeData/ERR009131_accepted_hits.bam
inst/extdata/genomeData/ERR009131_accepted_hits.bam.bai
inst/extdata/genomeData/ERR009138_accepted_hits.bam
inst/extdata/genomeData/ERR009138_accepted_hits.bam.bai
inst/extdata/genomeData/ERR009144_accepted_hits.bam
inst/extdata/genomeData/ERR009144_accepted_hits.bam.bai
inst/extdata/genomeData/ERR009145_accepted_hits.bam
inst/extdata/genomeData/ERR009145_accepted_hits.bam.bai
inst/extdata/genomeData/ERR009148_accepted_hits.bam
inst/extdata/genomeData/ERR009148_accepted_hits.bam.bai
inst/extdata/genomeData/ERR009151_accepted_hits.bam
inst/extdata/genomeData/ERR009151_accepted_hits.bam.bai
inst/extdata/genomeData/ERR009152_accepted_hits.bam
inst/extdata/genomeData/ERR009152_accepted_hits.bam.bai
inst/extdata/genomeData/ERR009153_accepted_hits.bam
inst/extdata/genomeData/ERR009153_accepted_hits.bam.bai
inst/extdata/genomeData/ERR009159_accepted_hits.bam
inst/extdata/genomeData/ERR009159_accepted_hits.bam.bai
inst/extdata/genomeData/ERR009161_accepted_hits.bam
inst/extdata/genomeData/ERR009161_accepted_hits.bam.bai
inst/extdata/genomeData/ERR009163_accepted_hits.bam
inst/extdata/genomeData/ERR009163_accepted_hits.bam.bai
inst/extdata/genomeData/ERR009164_accepted_hits.bam
inst/extdata/genomeData/ERR009164_accepted_hits.bam.bai
inst/extdata/genomeData/ERR009167_accepted_hits.bam
inst/extdata/genomeData/ERR009167_accepted_hits.bam.bai
inst/extdata/genomeData/SRR031812_accepted_hits.bam
inst/extdata/genomeData/SRR031812_accepted_hits.bam.bai
inst/extdata/genomeData/SRR031835_accepted_hits.bam
inst/extdata/genomeData/SRR031835_accepted_hits.bam.bai
inst/extdata/genomeData/SRR031867_accepted_hits.bam
inst/extdata/genomeData/SRR031867_accepted_hits.bam.bai
inst/extdata/genomeData/SRR031868_accepted_hits.bam
inst/extdata/genomeData/SRR031868_accepted_hits.bam.bai
inst/extdata/genomeData/SRR031900_accepted_hits.bam
inst/extdata/genomeData/SRR031900_accepted_hits.bam.bai
inst/extdata/genomeData/SRR031904_accepted_hits.bam
inst/extdata/genomeData/SRR031904_accepted_hits.bam.bai
inst/extdata/genomeData/SRR031914_accepted_hits.bam
inst/extdata/genomeData/SRR031914_accepted_hits.bam.bai
inst/extdata/genomeData/SRR031936_accepted_hits.bam
inst/extdata/genomeData/SRR031936_accepted_hits.bam.bai
inst/extdata/genomeData/SRR031958_accepted_hits.bam
inst/extdata/genomeData/SRR031958_accepted_hits.bam.bai
inst/extdata/genomeData/SRR031960_accepted_hits.bam
inst/extdata/genomeData/SRR031960_accepted_hits.bam.bai
man
man/analyzeChr.Rd
man/annotateRegions.Rd
man/calculatePvalues.Rd
man/calculateStats.Rd
man/coerceGR.Rd
man/collapseFullCoverage.Rd
man/coverageToExon.Rd
man/createBw.Rd
man/createBwSample.Rd
man/define_cluster.Rd
man/derfinder-deprecated.Rd
man/derfinder-package.Rd
man/extendedMapSeqlevels.Rd
man/filterData.Rd
man/findRegions.Rd
man/fullCoverage.Rd
man/genomeData.Rd
man/genomeDataRaw.Rd
man/genomeFstats.Rd
man/genomeInfo.Rd
man/genomeRegions.Rd
man/genomicState.Rd
man/getRegionCoverage.Rd
man/getTotalMapped.Rd
man/loadCoverage.Rd
man/makeGenomicState.Rd
man/makeModels.Rd
man/mergeResults.Rd
man/preprocessCoverage.Rd
man/railMatrix.Rd
man/rawFiles.Rd
man/regionMatrix.Rd
man/sampleDepth.Rd
tests
tests/test-all.R
tests/testthat
tests/testthat/test_ER_level.R
tests/testthat/test_Fstats.R
tests/testthat/test_annotation.R
tests/testthat/test_data.R
tests/testthat/test_findRegions.R
tests/testthat/test_misc.R
vignettes
vignettes/derfinder-quickstart.Rmd
vignettes/derfinder-users-guide.Rmd
derfinder documentation built on May 20, 2017, 10:40 p.m.